Dear Galal & Khalil,
You have tried to give a logical picture how mathematics has become effective in physics, and suggest the need for new mathematical inventions to solve the hitherto unsolved problems. You say correctly, "A great mystery about nature is that we can describe the same phenomenon with different mathematical formulations". Have you thought of the reverse possibility? A unique mathematical equation can have different physical interpretations. Refer my essay: A physicalist interpretation of the relation between Physics and Mathematics.
Are there any mathematical laws? Or are there only mathematical structures? I would answer that both exist, and there should be a clear distinction between the two: mathematical laws are discovered; but mathematical structures are invented. The laws are fundamental and eternal, that even an omnipotent creator cannot defy the laws. The structures depend on axioms, which are nothing but 'assigned properties'. But the evolution of the structure follows the eternal mathematical laws.
The same thing is true for the physical world. The physical world has certain properties; but its evolution (the series of changes) depends solely on mathematical laws, and this leads to structures that are mathematically explainable. We try to explain the physical world based on axioms (assigned properties). To arrive at these properties, we depend on 'mathematical relations' based on the observable natural structures. However, this can be tricky. My essay deals with this. If the assigned properties are correct, we will be able to explain everything.